Figure 1: MDS plot using all samples. Of these, samples GR.F3, WT.F3 and TktDfWT.F3 stand out as potential outliers.
Figure 2: Barplot of Total DEGs observed with edgeR when using all samples.
Figure 3: PCA of GR.F CxDf DEGs. Testing if GR.F3 is an outlier library.
Figure 4: PCA of GR.F CxOE DEGs. Testing if GR.F3 is an outlier library.
Figure 5: PCA of GR.FC x WT.FC DEGs. Testing if GR.F3 and WT.F3 are outlier libraries.
Figure 6: PCA of WT.F CxDf DEGs. Testing if WT.F3 and TktDfWT.F3 are outlier libraries.
Figure 7: PCA of WT.F CxOE DEGs. Testing if WT.F3 is an outlier library.
Figure 8: PCA of TktDfGR.F x TktDfWT.F DEGs. Testing if TktDfWT.F3 is an outlier library.
Figure 9: MDS plot using all samples, with the TEs and outlier libraries removed.
Figure 10: Barplot of Total DEGs found when using all samples with the TEs and outlier libraries removed.
Figure 11: MDS plot when the female samples are processed alone. The TEs and outlier libraries are removed.
Figure 12: MDS plot when the male samples are process alone only. The TEs are removed.
Figure 13: Barplot of Total DEGs when male and female samples are processed separately. The TEs and outlier libraries were removed.
Figure 14: Barplot of Total DEGs for each comparison under the different trimming conditions. Different trimming conditions were: (1) all samples processed together with no TEs or outlier libraries removed; (2) trimmed data with TEs and outlier libraries removed, male and female samples processed together; (3) trimmed data with TEs and outlier libraries removed, male and female samples processed separately.